Order 66 survivors.

Marc Sumerak's The Secrets of the Clone Troopers addresses this issue head-on. An in-universe of the clones from the perspective of Captain Rex, it features a section on Order 66 in which he wishes he'd been one of the strong ones who'd successfully resisted it.

"Even though Order 66 was designed to be a directive that we couldn't resist, not every clone ended up pulling the trigger. Some, like my friends in Clone Force 99, were less susceptible to the inhibitor chip's influence, due to their genetic augmentations. Others were simply strong enough to resist, at least until their Jedi general could escape."

This corresponds with previous hints in Star Wars: The Bad Batch that suggested the mutant clones of Clone Force 99 weren't the only ones to resist Order 66.

What This Order 66 Revelation Means For Star Wars

Rex is being too hard on himself in The Secrets of the Clone Troopers; in truth, he set the precedent for this idea at the end of Star Wars: The Clone Wars season 7, when he battled against the urge to open fire on Ahsoka Tano. Although his resistance was ultimately unsuccessful, his struggle did help Ahsoka realize something was wrong, and she was able to figure out the problem and remove Rex's chip. Skilled and powerful Jedi only needed a moment's notice to save their lives.

This may even explain why some of the Order 66 survivors have felt so random. It makes sense for Yoda to sense the deaths of Jedi across the galaxy and defend himself, but the Wookiee Jedi Gungi - barely a Padawan - is much more unlikely. It seems, though, that Order 66 was a lot more chaotic than we'd thought, and potentially many more Jedi survived.

Our Take On Order 66's Survivors

This subtle retcon has been coming for quite some time, and fits well with what we've seen before. Order 66 was still a horrific success, an act of genocide committed against the Jedi. If even 2% of the Jedi survived, that would still mean 9,800 Jedi were killed in an instant. It must be noted this is roughly in line with George Lucas' own plans, because his sequel trilogy plans saw Luke Skywalker discover 50-100 Jedi who'd survived beyond Return of the Jedi.

This further helps explain why Palpatine turned on the clones. He would probably have been fine with maintaining a clone army whose loyalty was unswerving, but the resistance of some clones would have concerned him. The great villain of Star Wars would prefer an Imperial army who had been indoctrinated, and whose brainwashing was under his own personal control.

Source: The Secrets of the Clone Troopers